comparison pick_plasmids_containing_genes.py @ 4:109b9d1e2e99 draft default tip

"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit 0f3fff91eb329adf437224eb8f7449853083b01e-dirty"

3:50640b06fca5

#!/usr/bin/env python

from __future__ import print_function

import argparse
import errno
import csv
import os
import re
import shutil
import sys

from pprint import pprint

def parse_screen_file(screen_file):
    screen = []
    with open(screen_file) as f:
        reader = csv.DictReader(f, delimiter="\t", quotechar='"')
        for row in reader:
            screen.append(row)
    return screen

def main(args):
    # create output directory
    try:
        os.mkdir(args.outdir)

                if re.search(gene['regex'], abricate_report_row['GENE']):
                    contigs_with_genes_of_interest.append(abricate_report_row['SEQUENCE'])
            f.seek(0)
            next(abricate_report_reader)

    # copy the corresponding plasmid fasta files into outdir        
    for contig in contigs_with_genes_of_interest:
        for plasmid in args.plasmids:
            copy_plasmid = False
            with open(plasmid, 'r') as f:
                for line in f:

                        copy_plasmid = True
            if copy_plasmid:
                print("\t".join([plasmid, "True"]))
                shutil.copy2(plasmid, args.outdir)

if __name__ == '__main__':
    parser = argparse.ArgumentParser()
    parser.add_argument("--plasmids", nargs='+', help="plasmid assemblies (fasta)")
    parser.add_argument("--concatenated_abricate_reports", help="abricate reports (tsv)")
    parser.add_argument("--abricate_report_screening_file", help="")

4:109b9d1e2e99

#!/usr/bin/env python

from __future__ import print_function

import argparse
import csv
import errno
import os
import re
import shutil


def parse_screen_file(screen_file):
    screen = []
    with open(screen_file) as f:
        reader = csv.DictReader(f, delimiter="\t", quotechar='"')
        for row in reader:
            screen.append(row)
    return screen


def main(args):
    # create output directory
    try:
        os.mkdir(args.outdir)

                if re.search(gene['regex'], abricate_report_row['GENE']):
                    contigs_with_genes_of_interest.append(abricate_report_row['SEQUENCE'])
            f.seek(0)
            next(abricate_report_reader)

    # copy the corresponding plasmid fasta files into outdir
    for contig in contigs_with_genes_of_interest:
        for plasmid in args.plasmids:
            copy_plasmid = False
            with open(plasmid, 'r') as f:
                for line in f:

                        copy_plasmid = True
            if copy_plasmid:
                print("\t".join([plasmid, "True"]))
                shutil.copy2(plasmid, args.outdir)


if __name__ == '__main__':
    parser = argparse.ArgumentParser()
    parser.add_argument("--plasmids", nargs='+', help="plasmid assemblies (fasta)")
    parser.add_argument("--concatenated_abricate_reports", help="abricate reports (tsv)")
    parser.add_argument("--abricate_report_screening_file", help="")